[gmx-users] Umberella sampling
ramezanpour.mohsen at gmail.com
Sun May 8 16:56:24 CEST 2011
Thank you for your complete explanation.
Please let me discribe where is NPT.cpt comes from:
Before doing Pulling step,I did an NPT step (as your tutorial) to generate
the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ...
Then I used NPT.gro for Pulling step to generate config0.gro and ...
After this step I used the NPT.cpt and config0.gro and .... to generate
umbrella0.tpr with grompp.
I think it is obvious now ,where is NPT.cpt come from!
I think my mistake is as you noted.I didn't use any -t option in
grompp,Then I lost the information for npt ensemble.
What do you think
Thanks in advance for your reply
On Sun, May 8, 2011 at 7:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> mohsen ramezanpour wrote:
>> Dear Dr.Justin
>> I didn't any equilibration for any windows! Because:
>> As I know the thermodynamics of the system had wroten in NPT.cpt file (for
>> example the velocities and etc).
> Then where does NPT.cpt come from? Presumably, if you have this file, you
> did some equilibration. I don't understand what you've done. If you want
> to rely on previous, equilibrium dynamics under an NPT ensemble, you must do
> equilibrium MD (not steered) for each configuration under the desired
> conditions, then pass the .cpt file to grompp -t when building the umbrella
> sampling input files.
> Then when I use that in grompp for each windows ,I expect the same
>> characteristics of system as before(At least the same T)!
> With "gen_vel = no" and no record of the prior state, this is not a
> reasonable expectation. You will get a temperature based on the initial
> forces present in the system (which determine initial velocities). The
> resulting temperature may or may not be identical to the previous state, but
> under the influence of a thermostat, you will reach the desired temperature.
> If you're attempting to follow my tutorial directly, at this point I think
> you should stop and consider the discussion I have in the tutorial on
> maintaining the ensemble:
> In the example system (one I know very well), it was satisfactory to simply
> "gen_vel = no" and allow these initial forces to govern the resulting
> dynamics. In many other cases (probably most), you should:
> 1. Generate your configurations (SMD, etc)
> 2. Run individual NPT simulations (or whatever ensemble) for each desired
> starting configuration (and thus obtain npt0.cpt, npt1.cpt, etc)
> 3. Initiate umbrella sampling windows using the npt*.cpt files from each
> Otherwise, skip step 2, use "gen_vel = yes" and discard the first few
> hundred ps as equilibration in each window.
> Actually after PULLING step I used the following commands:
>> grompp -f umbrella.mdp -c config0.gro -p complex.top -o
>> umbrella0.tpr -n index.ndx
>> mdrun -v -deffnm umbrella0 -px pullx0.xvg -pf pullf0.xvg -cpi
>> what is your point of view now?
> These commands do not necessarily preserve the ensemble. Without providing
> suitable information to grompp -t, the initial state is lost. I still don't
> know where NPT.cpt comes from. You say you're running grompp immediately
> after pulling, which is a non-equilibrium ensemble that you don't want to
> preserve as input into umbrella sampling. That, and likely the settings in
> SMD vs. US are different, so if NPT.cpt corresponds to your SMD simulation,
> you probably don't want to be using that for all your umbrella sampling
> windows, as the information it contains is for one single snapshot somewhere
> along the SMD run. If this is not the case, and you've generated NPT.cpt in
> some other manner, you will have to explain where it came from.
> What do you think if I use NPT.enr OR NPT.trr OR in
>> grompp(especially NPT.enr) ?
> Not necessary. Using .cpt files is more accurate.
> Because all of information about NPT step are included in this files.
> Note entirely. The differences between using .edr + .trr vs. .cpt alone
> are very small, but using a .cpt file is the most rigorously correct way to
> maintain the ensemble.
> Thanks in advance for your
>> On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>> mohsen ramezanpour wrote:
>> Dear Dr.Justin
>> Regarding doing umbrella sampling:
>> I used gen_vel =no
>> and I prefer to use from thermodynamics of system in NPT.cpt
>> Although the T and P were as I did set in NPT.mdp file (T=310
>> ,P=1 bar)
>> But their values in my umbrela.log files are not as before (for
>> example P=-8.434578e+1)
>> Where did I wrong?
>> I have no clue. You didn't provide your commands or any evidence
>> that the prior ensemble was to be maintained. If you have done NPT
>> equilibration in each window, then pass the .cpt file to grompp and
>> the ensemble should be preserved in each window. Note that an
>> instantaneous pressure value means nothing, as discussed weekly on
>> this list and online:
>> It is the average that is most meaningful.
>> -- ========================================
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> -- gmx-users mailing list gmx-users at gromacs.org
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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